TARGETED GENE THERAPY
Subject:TGR-Non Disease Specific
(The following material is presented in Ascending Date Order)
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Researcher Name shown is my estimate of Principal Researcher
DB Key:2001-INV-A
Doc:Web Page Article
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:How it works.
1/1/2001-----Davidson College-----Davidson College
Title:What is Chimeraplasty?
Link:http://www.bio.davidson.edu/courses/Molbio/MolStudents/spring2000/roberts/Pages/Chimeraplasty.html
Snippet:
For in vivo repair, the oligos can be attached to organ-specific ligands, as has been performed by Li-Wen Lai at the University of Arizona in Tucson (Smaglik 2000). Liposomes and synthetic polymers are also used to deliver chimeric molecules to the appropriate cells or tissue (Stephenson 1999). In plants, microscopic gold particles are coated with the chimeric molecules and fired into cells (Coghlan 1999). In all cases, the oligos that enter the nucleus can repair point mutations within the cell after pairing with their sequence-specific target DNA (Fig. 2) by causing the cell's repair machinery to perform mismatch repair on the point mutation (Cole-Strauss and others 1999). After correction, the chimera decays, leaving the corrected gene (Fig. 3) (Coghlan 1999).
DB Key:2001-INV-C
Doc:Abstract
Vector:ODN Oligodeoxynucleotides
Experiment:Failed or Not Applicable
Of Note:are capable of correcting a single point mutation (G to A) in the mutant beta-galactosidase gene
3/1/2001-----Yoon, Kyonggeun-----Thomas Jefferson University
Title:Targeted gene correction by small single-stranded oligonucleotides in mammalian cells
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11313816&dopt=Abstract
Snippet:
Surprisingly, these short single-stranded oligonucleotides (ODN) showed a similar gene correction frequency to chimeric RNA-DNA oligonucleotide, measured using the same system. The in vitro gene correction induced by ODN in nuclear extracts was not dependent on the length or polarity of the oligonucleotide. In contrast, the episomal and chromosomal gene corrections were highly dependent on the ODN length and polarity
DB Key:2001-INV-E
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:Here, we describe the activity of the synthetic vectors in a mammalian cell system
3/13/2001-----Kmiec EB-----University of Delaware
Title:Targeted gene repair in mammalian cells using chimeric RNA/DNA oligonucleotides and modified single-stranded vectors
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11752645&dopt=Abstract
Snippet:
Some of these vectors, including chimeric RNA/DNA oligonucleotides and modified single-stranded oligonucleotides, have shown promise in the specific alteration of a single base at an exact position within the gene. Here, we describe the activity of the synthetic vectors in a mammalian cell system.
DB Key:2001-INV-G
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:None
4/1/2001-----Kmiec EB-----University of Delaware
Title:The potential of nucleic acid repair in functional genomics
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11283588&dopt=Abstract
Snippet:
Chimeric RNA/DNA oligonucleotides have been used successfully to correct point and frameshift mutations in cells as well as in animal and plant models. This approach is one of several nucleic acid repair technologies that will help elucidate the function of newly discovered genes. Understanding the mechanisms by which these different technologies direct gene alteration is essential for progress in their application to functional genomics.
DB Key:2001-INV-J
Doc:Nature Biotechnology (2001) 19:305-306
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:To date, no mutation corrections have been observed. Attempts to alter
same epidermolysis bullosa genes in lymphocytes also failed. In addition, efforts
reproduce RDO experiments described in the literature, such as ß-globin
lymphocytes and coagulation factor IX in liver cells, have also been unsuccessful.
these latter cases, however, the less sensitive PCR/restriction-fragment-
polymorphism analysis system was used to detect sequence alterations.
6/1/2001-----Steege, Gerrit van der-----University of Groningen, Netherlands
Title:Persistent failures in gene repair
Link:http://www.ub.rug.nl/eldoc/dis/medicine/p.h.l.schuilenga-hut/c5.pdf
Snippet:
We believe that the persistent failure to implement the RDO technology is
noteworthy. The complete lack of success hampers further studies and frustrates the
usage of this theoretically tempting method. We would like to stress that, despite our
disappointing experiences, we do not denounce the RDO technology as being
invalid or objectionable. However, it may be of general concern, that a broad
application of this technique is still to be awaited, despite the number and the extent
positive reports, especially of some in vivo studies (Bartlett et al., 2000; Kren et
DB Key:2001-INV-L
Doc:European Journal of Dermatology
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:can correct this mutation in albino mouse melanocytes in culture [15].
8/1/2001-----Gupta, S.-----University of Pennsylvania School of Medicine
Title:Hair follicle as a target for gene therapy
Link:http://www.john-libbey-eurotext.fr/articles/ejd/11/4/353-6/
Snippet:
One topical approach for permanent correction of at least single base pair mutations stems from work on RNA-DNA oligonucleotides (RDO). Alexeev and Yoon [15] demonstrated that RDOs encoding for the correction of a single base pair mutation in tyrosinase can correct this mutation in albino mouse melanocytes in culture [15]. We then showed that this same RDO administered by topical application using liposomes can correct the albino mutation in vivo [16] in mice. After application, several pigmented hairs are detected in treated areas. These results demonstrate that topical lipoplex can also target melanocytes within the follicle. Ultimately, for RDO technology to become useful for therapeutic purposes in skin, its low efficiency will have to improve, and keratinocytes will have to be targeted.
DB Key:2001-INV-O
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:Here, the utility of this vector is expanded into Saccharomyces cerevisiae
10/15/2001-----Kmiec EB-----University of Delaware
Title:In vivo gene repair of point and frameshift mutations directed by chimeric RNA/DNA oligonucleotides and modified single-stranded oligonucleotides
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11600713&dopt=Abstract
2nd Link:http://nar.oupjournals.org/cgi/content/abstract/29/20/4238?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=Kmiec+EB&searchid=1032104998174_674&stored_search=&FIRSTINDEX=0&sortspec=Score+desc+PUBDATE_SORTDATE+desc&journalcode=nar
Snippet:
Among the most promising vectors is chimeric oligonucleotide (CO), a double-stranded, RNA-DNA hybrid molecule folded into a double hairpin conformation: by using the cell's DNA repair machinery, the CO directs nucleotide exchange as episomal and chromosomal DNA. Systematic dissection of the CO revealed that the region of contiguous DNA bases was the active component in the repair process, especially when the single-stranded ends were protected against nuclease attack. Here, the utility of this vector is expanded into Saccharomyces cerevisiae. An episome containing a mutated fusion gene encoding hygromycin resistance and eGFP expression was used as the target for repair
DB Key:2001-INV-Q
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:Letter - content not available
11/1/2001-----Albuquerque-Silva J-----Université Libre de Bruxelles
Title:Chimeraplasty Validation
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11689838&dopt=Abstract
Disease Information:http://www.medterms.com/script/main/Art.asp?li=MNI&ArticleKey=9736
Snippet:
Content of Letter not given
DB Key:2001-INV-P
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:NPRO
11/1/2001-----Kmiec EB-----University of Delaware
Title:Eric B. Kmiec, Ph.D.
Link:http://www.dbi.udel.edu/kmiec.html
2nd Link:http://www.naprobio.com/news/press_releases/9=18=01_PDF.pdf
Snippet:
Biography:
DB Key:2001-INV-R
Doc:Web Page Article
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:Brown has visited Yoon
11/1/2001-----Brown, Brian PhD-----Queen's University
Title:Evaluation of a Small Oligonucleotide-based Method of Genetic Manipulation
Link:http://www.path.queensu.ca/queens/labs/lillicrap/brown/brown.html
Snippet:
Evaluation of a Small Oligonucleotide-based Method of Genetic Manipulation
I worked on a novel method for inducing a single base pair change in situ, called chimeraplasty. The technique involves the use of a 68mer RNA-DNA oligonucleotide (RDO) which has complementary sequence to a target area of the genome. When the RDO enters the cell nucleas it pairs with complete homology to its target genomic region, except at one nucleotide. The nucleotide mispair distorts the DNA helix, and the cell's mismatch repair enzymes respond by excising one of the two nucleotides, either from the RDO or from the host genome, and they replace it with a nucleotide that will result in a proper Watson-Crick base pair. Hence, the RDO is able to direct an in situ nucleotide exchange. Click here for a diagram of the chimeraplasty process. (Note: Images from Kimeragen)
DB Key:2001-INV-S
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:3 Improvements suggested
11/1/2001-----Wu XS-----Chinese Academy of Medical Sciences and Peking Union Medical College
Title:Prospects of chimeric RNA-DNA oligonucleotides in gene therapy
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11702006&dopt=Abstract
Snippet:
To overcome this difficulty, three main aspects should be considered. One is designing a more effective structure of the oligonucleotide. Trials have included lengthening the homologous region, displacing the mismatch on the chimeric strand and inventing a novel thioate-modified single-stranded DNA, which was demonstrated to be more active than the primary chimera in cell-free extracts. The second aspect is optimizing the delivery system. Producing synthetic carriers for efficient and specific transfection is demanding, especially for treatment in vivo where targeting is difficult. The third and most important aspect lies in the elucidation of the mechanism of the strategy
DB Key:2002-INV-A
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:Six recent studies of chimeric are reviewed
1/15/2002-----Lai LW-----University of Arizona Health Sciences Center
Title:Chimeric RNA/DNA oligonucleotide-based gene therapy
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11841612&dopt=Abstract
Disease Information:http://www.medterms.com/script/main/Art.asp?li=MNI&ArticleKey=9736
Snippet:
METHODS: Six recent studies of chimeric RNA/DNA oligonucleotide-based gene therapy in genetic disease models are reviewed. Chimeric RNA/DNA oligonucleotides, complementary to 25 to 30 residues of genomic DNA flanking the mutation site with the exception of a mismatch in the center, were delivered via different routes and delivery vehicles to target different tissues and organs. Corrections of the mutation at genotypic and phenotypic levels were assessed using various methods, including allele-specific polymerase chain reaction assay, restriction enzyme digestion, colony-lifting assays, sequencing, Northern and Western blot analyses, enzyme activity assay, immunohistochemical staining, and functional studies
DB Key:2002-INV-B
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:In particular, we discuss technologies based on chimeric RNA/DNA oligonucleotides, single-stranded and triplex-forming oligonucleotides, and small fragment homologous replacement
2/1/2002-----Steer CJ-----University of Minnesota
Title:Gene repair and transposon-mediated gene therapy
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11897868&dopt=Abstract
2nd Link:http://stemcells.alphamedpress.org/cgi/content/abstract/20/2/105
Snippet:
While each of these approaches is different, they all share a number of common characteristics, including the need for efficient delivery of nucleic acids to the nucleus. In addition, we review the potential application of a novel and exciting nonviral gene augmentation strategy--the Sleeping Beauty transposon system
DB Key:2002-INV-C
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:None
2/14/2002-----Kmiec EB-----University of Delaware
Title:Targeted gene repair and its application to neurodegenerative disorders
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11856524&dopt=Abstract
Snippet:
Synthetic DNA oligonucleotides can direct the exchange of single nucleotides within coding regions of mammalian genes by hybridizing to their complementary sequence in the chromosome and creating a recombination joint structure with a single mismatched base pair. Inherent DNA repair processes recognize the mismatch and resolve it using the DNA sequence of the oligonucleotide vector as the template. This gene surgery approach can be used to repair mutations or to disrupt tri-nucleotide repeats in dysfunctional genes responsible for neurological disorders
DB Key:2002-INV-D
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:Homologous nucleic acid sequences can correct mutations by inducing recombination or mismatch repair. Recently, encouraging data have been presented using both short DNAfragments (SDFs) and RNA-DNA oligonucleotides (RDOs) in experimental strategies to realize clinical gene correction
3/1/2002-----Porteous DJ-----University of Edinburgh
Title:Functional correction of episomal mutations withshort DNA fragments and RNA-DNA oligonucleotides
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11933220&dopt=Abstract
Snippet:
RDOs only corrected the reporter in a cell line that overexpresses RAD51
DB Key:2002-INV-E
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:The reaction mechanism has only recently come to light, and parameters that confer a level of control on the frequency of repair are still being defined in model genetic systems
4/1/2002-----Kmiec EB-----University of Delaware
Title:The 'biased' evolution of targeted gene repair
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12044039&dopt=Abstract
Snippet:
Regulatory factors, such as strand bias, vector length, and the phase of the cell cycle in which targeting events take place, are now appreciated.
DB Key:2002-INV-F
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:Airway Epithelial Cells
5/1/2002-----Aran JM.-----Centre de Genetica Medica i Molecular, Institut de Recerca Oncologica, Hospital Duran i Reynals, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
Title:Non-viral vector-mediated uptake, distribution, and stability of chimeraplasts in human airway epithelial cells.
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12112648&dopt=Abstract
Snippet:
Moreover, significant chimeraplast degradation was detected 24 h after transfection with both PEI polyplexes and Cytofectin lipoplexes
DB Key:2002-INV-C11
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:Overview of TGR
5/9/2002-----Dickson, George J., Ph.D.-----Royal Holloway-University of London
Title:Gene repair and mutagenesis mediated by chimeric RNA-DNA oligonucleotides: chimeraplasty for gene therapy and conversion of single nucleotide polymorphisms (SNPs).
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12009417&dopt=Abstract
Snippet:
Although the only gene defects that can be corrected by chimeraplasty are point mutations, and the correction frequencies are variable, it has been observed that intracellular delivery of oligonucleotides is likely to be more efficient than that of plasmid DNA or viral vectors. Furthermore, corrected genes are expressed from their autologous promoters, thus ensuring correct spatial and temporal expression. Here we report on the recent progress made in the field of chimeraplasty, and the problems encountered.
DB Key:2002-INV-J
Doc:Abstract
Vector:GOREC Guided Homologous Recombination
Experiment:Failed or Not Applicable
Of Note:GOREC - Here we describe a new method named GOREC (guided homologous recombination) which shares similar gene targeting, but has notable difference in the concept with the previous method. It is made of a homing device (TFO) and a donor DNA for effecting distinct functions. They are linked together by non-covalent or covalent interaction.
6/1/2002-----Maurisse R-----Laboratoire de Biophysique, UMR8646 CNRS-Museum National d'Histoire Naturelle,
Title:A new method (GOREC) for directed mutagenesis and gene repair by homologous recombination.
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12032692&dopt=Abstract
Snippet:
Here we describe a new method named GOREC (guided homologous recombination) which shares similar gene targeting, but has notable difference in the concept with the previous method. It is made of a homing device (TFO) and a donor DNA for effecting distinct functions. They are linked together by non-covalent or covalent interaction. This modular concept allows guidance of either an oligonucleotide (ODN, RDO) or a small DNA fragment to the target site for homologous replacement. Therefore, the triple helix site can be hundreds of base pairs away from the target site. An episomal assay for proof-of-principle study will be presented and discussed.
DB Key:2002-INV-H
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:A number of strategies, including RNA-DNA oligonucleotides (RDOs) and short DNA fragments (SDFs), show promise in improving the efficiency of gene correction. We are using GFP as a reporter for gene repair in living cells. A single base substitution was introduced into GFP to create a nonsense mutation (STOP codon, W399X). RDOs and SDFs are used to repair this mutation episomally in transient transfections and restore green fluorescence.
6/1/2002-----Stevenson BJ-----University of Edinburgh
Title:Optimising gene repair strategies in cell culture
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12032691&dopt=Abstract
Snippet:
The correction efficiency is determined by FACS analysis. SDFs appear to correct GFP W399X in a number of different cell lines (COS7, A549, HT1080, HuH-7), although all at a similar low frequency ( approximately 0.6% of transfected cells). RDOs correct only one of our cell lines significantly (HT1080-RAD51), these cells overexpress the human RAD51 gene; the bacterial RecA homologue. The GFP W399X reporter is a fusion gene with hygromycin (at the 5' end), this has allowed us to make stable cell lines (A549, HT1080) to study genomic correction. Initial studies using our correction molecules show only low efficiencies of genomic repair ( approximately 10(-4)). Polyethylenimine (PEI) is used to deliver RDOs and SDFs into mammalian cells in culture for our study. We have used fluorescently labelled RDOs and SDFs to study the effectiveness of this process. FACS analysis of transfected nuclei implied efficient delivery (>90%) both with SDFs and RDOs. However, confocal fluorescence microscopy suggests that a large proportion of the complexed RDO/SDF appears to remain outside the nucleus (or attached to the nuclear membrane). On the basis of these data we are assessing new delivery methods and factors that may alter recombination status to optimise gene repair.
DB Key:2002-INV-L
Doc:Abstract
Vector:RDO RNA-DNA chimeric oligonucleotide
Experiment:Failed or Not Applicable
Of Note:Modified single-stranded DNA oligonucleotides can direct nucleotide exchange in Saccharomyces cerevisiae. Point and frameshift mutations are corrected in a reaction catalyzed by cellular enzymes involved in various DNA repair processes
6/22/2002-----Kmiec EB-----University of Delaware
Title:Strand bias in targeted gene repair is influenced by transcriptional activity
Link:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11997519&dopt=Abstract
2nd Link:http://mcb.asm.org/cgi/content/abstract/22/11/3852
Snippet:
The choice of which strand to target is a reaction parameter that can be controlled, so here we investigate the properties of strand bias in targeted gene repair. An in vivo system has been established in which a plasmid containing an actively transcribed, but mutated, hygromycin-enhanced green fluorescent protein fusion gene is targeted for repair and upon conversion will confer hygromycin resistance on the cell |
